Spider: Software for protein identification from sequence tags with de novo sequencing error

Journal of Bioinformatics and Computational Biology

Volumn 3, Issue 3, 2005, Pages 697-716

  Han, Yonghua ^a   Ma, Bin ^a   Zhang, Kaizhong ^a  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

Database search; De novo sequencing; Protein identification; Sequence tags

Indexed keywords

AMINO ACID; PEPTIDE; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; INTERNET; PROTEIN ANALYSIS; PROTEIN DATABASE; SEQUENCE HOMOLOGY; TANDEM MASS SPECTROMETRY;

ALGORITHMS; EXPRESSED SEQUENCE TAGS; MASS SPECTROMETRY; PEPTIDE MAPPING; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

ARANEAE;

EID: 22544465253     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720005001247     Document Type: Article

References (31)

1. Aebersold R, Mann M, Mass spectrometry-based proteomics, Nature 422:198-207 2003.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, Basic local alignment search tool, J Mol Biol 215:403-410, 1990.
3. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Res 25:3389-3402, 1997.
4. Bafna V, Edwards N, On de novo interpretation of tandem mass spectra for peptide identification, RECOMB 2003, Berlin, Germany, 2003.
5. Bartels C, Fast algorithm for peptide sequencing by mass spectroscopy, Biomed Environ Mass Spectrom 19:363-368, 1990.
6. Chen T, Kao M-Y, Tepel M, Rush J, Church G, A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry, J Comp Biology 8(3):325-337, 2001.
7. Dančík V, Addona T, Clauser K, Vath J, Pevzner P, De novo protein sequencing via tandem mass-spectrometry, J Comp Biology 6:327-341, 1999.
8. Eng JK, McCormack AL, Yates JR, III An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database, J Am Soc Mass Spectrom 5:976-989, 1994.
9. Fernández-de-Cossío J, Gonzalez J, Betancourt L, Besada V, Padron G, Shimonishi Y, Takao T, Automated interpretation of high-energy collision-induced dissociation spectra of singly-protonated peptides by "SeqMS", a software aid for de novo sequencing by MS/MS, Rapid Commun Mass Spectrom 12:1867-1878, 1998.
10. Han Y, Ma B, Zhang K, Gapped sequence tag query for improving de novo sequencing results, 2003, ASMS.
11. Henikoff S, Henikoff JG, Amino acid substitution matrices from protein blocks, Proc Natl Acad Sci USA 89:10915-10919, 1992.
12. Hines WM, Falick AM, Burlingame AL, Gibson BW, Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra, J Am Sco Mass Spectrom 3:326-336, 1992.
13. Huang L, Jacob RJ, Pegg SC-H, Baldwin MA, Wang CC, Burlingame AL, Babbitt PC, Functional Assignment of the 20 S Proteasome from Trypanosoma brucei Using Mass Spectrometry and New Bioinformatics Approaches, J Biol Chem 276(30):28327-28339 2001.
14. Lu B, Chen T, A suboptimal algorithm for de novo peptide sequencing via tandem mass spectrometry, J Comp Biology 10:1-12, 2003.
15. Ma B, Tromp J, Li M, PatternHunter: Faster and more sensitive homology search, Bioinformatics 18(3):440-445, 2002.
16. Ma B, Zhang K, Lajoie G, Doherty-Kirby A, Hendrie C, Liang C, Li M, PEAKS: Powerful software for peptide de novo sequencing by MS/MS, Commun Mass Spectrom 17(20):2337-2342, 2003.
17. Ma B, Zhang K, Liang C, An effective algorithm for the peptide de novo sequencing from MS/MS spectrum, to appear in Journal of Computer and System Sciences.
18. Mackey AJ, Haystead TAJ, Pearson WR, Getting more for less: Algorithms for rapid protein identification with multiple short peptide sequences, Mol Cell Proteomics 1:139-147, 2002.
19. Mann M, Wilm M, Error-tolerant identification of peptides in sequence databases by peptide sequence tags, Anal Chem 66:4390-4399, 1994.
20. Pearson WR, Lipman DJ, Improved tools for biological sequence comparison, Proc Natl Acad Sci USA 85:2444-2448, 1988.
21. Pegg SC, Babbitt PC, Shotgun: Getting more from sequence similarity searches, Bioinformatics 15:729-740, 1999.
22. Perkins DN, Pappin DJC, Creasy DM, Cottrell JS, Probability-based protein identification by searching sequence database using mass spectrometry data, Electrophoresis 20:3551-3567, 1999.
23. Pevzner PA, Dančík V, Tang C, Mutation tolerant protein identification by mass spectrometry, J Comp Biology 6:777-787, 2000.
24. Sakurai T, Matsuo T, Matsuda H, Katakuse I, Paas3: A computer program to determine probable sequence of peptides from mass spectrometric data, Biomed Mass spectrum 11(8):396-399, 1984.
25. Searle BC, Dasari S, Turner M, Reddy AP, Choi D, Wilmarth PA, McCormack AL, David LL, Nagalla SR, High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results, Anal Chem 76:2220-2230, 2004.
26. Shevchenko A, Sunyaev S, Loboda A, Shevchenko A, Bork P, Ens W, Standing KG, Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching, Anal Chem 73(9):1917-1926, 2001.
27. Tabb DL, Saraf A, Yates JR, III GutenTag: High-throughput sequence tagging via an empirically derived fragmentation model, Anal Chem 75:6415-6421, 2003.
28. Taylor JA, Johnson RS, Sequence database searches via de novo peptide sequencing by tandem mass spectrometry, Rapid Commun Mass Spectrom 11:1067-1075, 1997.
29. Taylor JA, Johnson RS, Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry, Anal Chem 73:2594-2604, 2001.
30. Uttenweiler-Joseph S, Neubauer G, Christoforidis S, Zerial M, Wilm M, Automated de novo sequencing of proteins using the differential scanning technique, Proteomics 1:668-682, 2001.
31. Yates JRI, Eng JK, McCormack AL, Schieltz D, Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database, Anal Chem 67:1426-1436, 1995.